Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 2249R

Calculation Name: 1CMX-A-Xray372

Preferred Name:

Target Type:

Ligand Name: amino-acetaldehyde

ligand 3-letter code: GLZ

PDB ID: 1CMX

Chain ID: A

ChEMBL ID:

UniProt ID: P0CG48

Base Structure: X-ray

Registration Date: 2023-03-13

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2548122.205729
FMO2-HF: Nuclear repulsion 2465229.317614
FMO2-HF: Total energy -82892.888116
FMO2-MP2: Total energy -83138.370835


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:6:ARG)


Summations of interaction energy for fragment #1(A:6:ARG)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-158.798-156.2520.232-0.865-1.913-0.002
Interaction energy analysis for fragmet #1(A:6:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.942 / q_NPA : 0.952
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A8VAL00.0080.0143.8221.5233.162-0.021-0.709-0.909-0.001
4A9VAL00.0290.0106.765-0.366-0.3660.0000.0000.0000.000
5A10PRO0-0.022-0.00510.3360.0140.0140.0000.0000.0000.000
6A11ILE00.0580.03012.4880.5510.5510.0000.0000.0000.000
7A12GLU-1-0.666-0.75814.816-11.626-11.6260.0000.0000.0000.000
8A13SER0-0.0150.00718.609-0.005-0.0050.0000.0000.0000.000
9A14ASN0-0.013-0.03120.9570.7160.7160.0000.0000.0000.000
10A15PRO00.0510.01722.184-0.370-0.3700.0000.0000.0000.000
11A16GLU-1-0.894-0.92723.297-11.396-11.3960.0000.0000.0000.000
12A17VAL00.0750.04617.769-0.190-0.1900.0000.0000.0000.000
13A18PHE0-0.030-0.02117.715-0.469-0.4690.0000.0000.0000.000
14A19THR00.009-0.01320.120-0.136-0.1360.0000.0000.0000.000
15A20ASN0-0.090-0.03419.862-0.265-0.2650.0000.0000.0000.000
16A21PHE00.015-0.01713.197-0.224-0.2240.0000.0000.0000.000
17A22ALA0-0.0090.00318.061-0.198-0.1980.0000.0000.0000.000
18A23HIS0-0.047-0.02520.3130.1780.1780.0000.0000.0000.000
19A24LYS10.8530.93416.78814.78714.7870.0000.0000.0000.000
20A25LEU0-0.021-0.01015.262-0.308-0.3080.0000.0000.0000.000
21A26GLY00.034-0.00819.111-0.015-0.0150.0000.0000.0000.000
22A27LEU0-0.067-0.00422.5180.4080.4080.0000.0000.0000.000
23A28LYS10.8790.91724.4579.3929.3920.0000.0000.0000.000
24A29ASN0-0.016-0.03127.863-0.071-0.0710.0000.0000.0000.000
25A30GLU-1-0.966-0.96829.420-8.127-8.1270.0000.0000.0000.000
26A31TRP0-0.026-0.00828.3140.1730.1730.0000.0000.0000.000
27A32ALA00.0360.01326.392-0.192-0.1920.0000.0000.0000.000
28A33TYR00.011-0.00721.344-0.056-0.0560.0000.0000.0000.000
29A34PHE0-0.017-0.00725.8770.1690.1690.0000.0000.0000.000
30A35ASP-1-0.851-0.93727.561-9.913-9.9130.0000.0000.0000.000
31A36ILE0-0.047-0.01928.4840.3060.3060.0000.0000.0000.000
32A37TYR00.002-0.01329.921-0.067-0.0670.0000.0000.0000.000
33A38SER0-0.023-0.03132.2810.0370.0370.0000.0000.0000.000
34A39LEU0-0.0050.00631.1960.0300.0300.0000.0000.0000.000
35A40THR0-0.037-0.03534.5750.0530.0530.0000.0000.0000.000
36A41GLU-1-0.864-0.91938.240-7.056-7.0560.0000.0000.0000.000
37A42PRO0-0.020-0.00539.782-0.058-0.0580.0000.0000.0000.000
38A43GLU-1-0.903-0.96641.667-6.510-6.5100.0000.0000.0000.000
39A44LEU00.0270.01437.387-0.049-0.0490.0000.0000.0000.000
40A45LEU0-0.045-0.00735.247-0.153-0.1530.0000.0000.0000.000
41A46ALA0-0.008-0.00138.099-0.015-0.0150.0000.0000.0000.000
42A47PHE0-0.107-0.04537.4760.0830.0830.0000.0000.0000.000
43A48LEU0-0.009-0.00431.613-0.217-0.2170.0000.0000.0000.000
44A49PRO0-0.0150.00333.1050.1860.1860.0000.0000.0000.000
45A50ARG10.8020.88434.1437.5717.5710.0000.0000.0000.000
46A51PRO0-0.034-0.03734.0580.1100.1100.0000.0000.0000.000
47A52VAL0-0.005-0.01529.692-0.195-0.1950.0000.0000.0000.000
48A53LYS10.8050.87828.7649.0419.0410.0000.0000.0000.000
49A54ALA00.0160.01524.413-0.201-0.2010.0000.0000.0000.000
50A55ILE0-0.0110.00125.7250.1610.1610.0000.0000.0000.000
51A56VAL0-0.036-0.01519.831-0.341-0.3410.0000.0000.0000.000
52A57LEU0-0.0050.00122.0890.4110.4110.0000.0000.0000.000
53A58LEU0-0.030-0.01518.454-0.616-0.6160.0000.0000.0000.000
54A59PHE00.0170.00520.7610.4750.4750.0000.0000.0000.000
55A60PRO00.0580.02520.716-0.698-0.6980.0000.0000.0000.000
56A61ILE0-0.075-0.02417.2190.0890.0890.0000.0000.0000.000
57A62ASN0-0.013-0.00620.445-0.208-0.2080.0000.0000.0000.000
58A78ASP-1-0.958-0.99328.419-9.637-9.6370.0000.0000.0000.000
59A79VAL00.0370.03024.5390.1510.1510.0000.0000.0000.000
60A80ILE0-0.0010.00620.052-0.361-0.3610.0000.0000.0000.000
61A81TRP0-0.035-0.02816.905-0.212-0.2120.0000.0000.0000.000
62A82PHE0-0.001-0.00514.009-0.311-0.3110.0000.0000.0000.000
63A83LYS10.8390.92912.01219.02619.0260.0000.0000.0000.000
64A84GLN0-0.047-0.0388.6620.5340.5340.0000.0000.0000.000
65A85SER0-0.054-0.0537.2670.5070.5070.0000.0000.0000.000
66A86VAL0-0.040-0.0102.733-5.893-5.4270.250-0.082-0.634-0.001
67A87LYS10.8640.9144.44329.51129.666-0.001-0.022-0.1320.000
68A88ASN0-0.008-0.0266.3030.1620.1620.0000.0000.0000.000
69A89ALA00.0150.0166.9921.4981.4980.0000.0000.0000.000
70A90CYS0-0.0470.0099.0380.7340.7340.0000.0000.0000.000
71A91GLY00.1070.04212.4000.7050.7050.0000.0000.0000.000
72A92LEU00.0160.0069.9910.5990.5990.0000.0000.0000.000
73A93TYR00.0360.0048.443-0.539-0.5390.0000.0000.0000.000
74A94ALA00.0120.03713.7310.7110.7110.0000.0000.0000.000
75A95ILE00.0320.03316.0970.7240.7240.0000.0000.0000.000
76A96LEU00.0150.00812.9850.5000.5000.0000.0000.0000.000
77A97HIS0-0.0180.00416.4770.4220.4220.0000.0000.0000.000
78A98SER00.0350.00519.4300.6720.6720.0000.0000.0000.000
79A99LEU00.0070.00819.4630.5470.5470.0000.0000.0000.000
80A100SER0-0.023-0.03719.3310.2440.2440.0000.0000.0000.000
81A101ASN0-0.086-0.04322.0110.3870.3870.0000.0000.0000.000
82A102ASN00.0230.00724.8660.7260.7260.0000.0000.0000.000
83A103GLN00.0450.01624.6570.1230.1230.0000.0000.0000.000
84A104SER0-0.024-0.00526.7180.1330.1330.0000.0000.0000.000
85A105LEU0-0.027-0.01227.0410.2520.2520.0000.0000.0000.000
86A106LEU00.0050.01122.578-0.140-0.1400.0000.0000.0000.000
87A107GLU-1-0.844-0.91125.914-8.951-8.9510.0000.0000.0000.000
88A108PRO0-0.054-0.02826.415-0.367-0.3670.0000.0000.0000.000
89A109GLY0-0.0120.00526.4220.1440.1440.0000.0000.0000.000
90A110SER0-0.025-0.00422.745-0.305-0.3050.0000.0000.0000.000
91A111ASP-1-0.874-0.95318.087-13.992-13.9920.0000.0000.0000.000
92A112LEU0-0.029-0.01617.535-0.484-0.4840.0000.0000.0000.000
93A113ASP-1-0.779-0.86519.825-10.758-10.7580.0000.0000.0000.000
94A114ASN0-0.040-0.02621.6880.4640.4640.0000.0000.0000.000
95A115PHE0-0.052-0.01615.880-0.122-0.1220.0000.0000.0000.000
96A116LEU0-0.002-0.00920.003-0.097-0.0970.0000.0000.0000.000
97A117LYS10.8610.90622.05210.59510.5950.0000.0000.0000.000
98A118SER00.0200.02221.6400.1210.1210.0000.0000.0000.000
99A119GLN0-0.0200.01417.8130.2700.2700.0000.0000.0000.000
100A120SER0-0.027-0.01022.7770.1520.1520.0000.0000.0000.000
101A121ASP-1-0.976-0.97226.237-10.295-10.2950.0000.0000.0000.000
102A122THR0-0.075-0.05923.8360.0780.0780.0000.0000.0000.000
103A123SER0-0.093-0.04026.1420.1630.1630.0000.0000.0000.000
104A124SER0-0.018-0.01720.7120.1950.1950.0000.0000.0000.000
105A125SER0-0.022-0.02518.7770.2900.2900.0000.0000.0000.000
106A126LYS10.9240.94722.05910.20410.2040.0000.0000.0000.000
107A127ASN0-0.043-0.03122.7230.1670.1670.0000.0000.0000.000
108A128ARG10.9681.00419.90813.81313.8130.0000.0000.0000.000
109A129PHE00.0700.02815.943-0.255-0.2550.0000.0000.0000.000
110A130ASP-1-0.834-0.92514.157-18.277-18.2770.0000.0000.0000.000
111A131ASP-1-0.802-0.86813.502-19.278-19.2780.0000.0000.0000.000
112A132VAL00.0380.0139.904-1.067-1.0670.0000.0000.0000.000
113A133THR0-0.028-0.02911.535-1.351-1.3510.0000.0000.0000.000
114A134THR00.015-0.00812.1910.3620.3620.0000.0000.0000.000
115A135ASP-1-0.829-0.8907.795-30.612-30.6120.0000.0000.0000.000
116A136GLN0-0.036-0.0138.558-2.910-2.9100.0000.0000.0000.000
117A137PHE00.0470.03110.3470.1500.1500.0000.0000.0000.000
118A138VAL00.0280.0197.6760.3880.3880.0000.0000.0000.000
119A139LEU0-0.028-0.0333.650-1.163-0.8770.004-0.052-0.2380.000
120A140ASN0-0.058-0.0437.419-0.582-0.5820.0000.0000.0000.000
121A141VAL00.1130.07910.7430.8760.8760.0000.0000.0000.000
122A142ILE0-0.023-0.0085.8800.5630.5630.0000.0000.0000.000
123A143LYS10.8150.9027.24327.40827.4080.0000.0000.0000.000
124A144GLU-1-0.942-0.9609.532-16.313-16.3130.0000.0000.0000.000
125A145ASN0-0.054-0.03412.0542.0242.0240.0000.0000.0000.000
126A146VAL00.005-0.0079.1160.2200.2200.0000.0000.0000.000
127A147GLN0-0.008-0.00711.3830.1320.1320.0000.0000.0000.000
128A148THR00.0590.03614.6060.3180.3180.0000.0000.0000.000
129A149PHE0-0.060-0.02310.3370.0740.0740.0000.0000.0000.000
130A150SER0-0.024-0.01013.371-0.102-0.1020.0000.0000.0000.000
131A151THR0-0.053-0.00915.2650.6570.6570.0000.0000.0000.000
132A152GLY00.0430.02218.610-0.297-0.2970.0000.0000.0000.000
133A153GLN0-0.122-0.07221.4000.3450.3450.0000.0000.0000.000
134A154SER0-0.080-0.06721.0110.1480.1480.0000.0000.0000.000
135A155GLU-1-0.947-0.97619.553-12.112-12.1120.0000.0000.0000.000
136A156ALA0-0.022-0.00714.707-0.308-0.3080.0000.0000.0000.000
137A157PRO00.0200.01013.986-0.075-0.0750.0000.0000.0000.000
138A158GLU-1-0.898-0.95110.930-19.371-19.3710.0000.0000.0000.000
139A159ALA0-0.023-0.0056.563-0.402-0.4020.0000.0000.0000.000
140A160THR0-0.042-0.0297.260-1.180-1.1800.0000.0000.0000.000
141A161ALA00.0060.0038.614-0.444-0.4440.0000.0000.0000.000
142A162ASP-1-0.874-0.92711.810-22.303-22.3030.0000.0000.0000.000
143A163THR00.0420.01213.3080.9580.9580.0000.0000.0000.000
144A164ASN0-0.050-0.01615.7840.5290.5290.0000.0000.0000.000
145A165LEU00.0210.03017.3070.6910.6910.0000.0000.0000.000
146A166HIS0-0.050-0.05814.370-1.544-1.5440.0000.0000.0000.000
147A167TYR00.001-0.03315.2360.8910.8910.0000.0000.0000.000
148A168ILE0-0.027-0.00317.372-0.554-0.5540.0000.0000.0000.000
149A169THR0-0.023-0.01719.7370.1070.1070.0000.0000.0000.000
150A170TYR0-0.035-0.03021.953-0.005-0.0050.0000.0000.0000.000
151A171VAL00.026-0.00224.564-0.026-0.0260.0000.0000.0000.000
152A172GLU-1-0.829-0.90927.276-9.017-9.0170.0000.0000.0000.000
153A173GLU-1-0.901-0.95027.259-10.062-10.0620.0000.0000.0000.000
154A174ASN0-0.071-0.02630.2570.5320.5320.0000.0000.0000.000
155A175GLY0-0.014-0.01333.2420.0700.0700.0000.0000.0000.000
156A176GLY0-0.063-0.01332.4500.1840.1840.0000.0000.0000.000
157A177ILE00.0300.02329.945-0.120-0.1200.0000.0000.0000.000
158A178PHE00.0230.00325.7060.0160.0160.0000.0000.0000.000
159A179GLU-1-0.690-0.78423.235-11.282-11.2820.0000.0000.0000.000
160A180LEU0-0.059-0.04020.130-0.246-0.2460.0000.0000.0000.000
161A181ASP-1-0.701-0.84016.715-16.123-16.1230.0000.0000.0000.000
162A182GLY00.0250.02814.022-0.110-0.1100.0000.0000.0000.000
163A183ARG10.8490.90310.66721.01521.0150.0000.0000.0000.000
164A184ASN00.0150.01614.6890.0850.0850.0000.0000.0000.000
165A185LEU0-0.014-0.02514.290-0.082-0.0820.0000.0000.0000.000
166A186SER0-0.068-0.03117.783-0.168-0.1680.0000.0000.0000.000
167A187GLY00.0040.01019.7800.5100.5100.0000.0000.0000.000
168A188PRO0-0.0220.00020.8410.0300.0300.0000.0000.0000.000
169A189LEU0-0.0120.00422.8830.2430.2430.0000.0000.0000.000
170A190TYR0-0.028-0.01325.6930.2840.2840.0000.0000.0000.000
171A191LEU0-0.005-0.01928.3010.0560.0560.0000.0000.0000.000
172A192GLY0-0.0030.00231.2080.2910.2910.0000.0000.0000.000
173A193LYS10.8780.92233.7807.5567.5560.0000.0000.0000.000
174A194SER00.0240.00334.741-0.045-0.0450.0000.0000.0000.000
175A195ASP-1-0.847-0.91436.529-6.925-6.9250.0000.0000.0000.000
176A196PRO0-0.049-0.03939.458-0.061-0.0610.0000.0000.0000.000
177A197THR0-0.117-0.05841.2400.1470.1470.0000.0000.0000.000
178A198ALA00.0080.01537.6480.0390.0390.0000.0000.0000.000
179A199THR0-0.071-0.06439.071-0.094-0.0940.0000.0000.0000.000
180A200ASP-1-0.763-0.86134.069-8.231-8.2310.0000.0000.0000.000
181A201LEU00.0280.01828.2540.1020.1020.0000.0000.0000.000
182A202ILE00.0270.01332.013-0.056-0.0560.0000.0000.0000.000
183A203GLU-1-0.896-0.90734.169-7.194-7.1940.0000.0000.0000.000
184A204GLN00.0510.04033.7240.2130.2130.0000.0000.0000.000
185A205GLU-1-0.837-0.92434.796-7.697-7.6970.0000.0000.0000.000
186A206LEU0-0.024-0.01333.425-0.081-0.0810.0000.0000.0000.000
187A207VAL00.0110.01029.234-0.237-0.2370.0000.0000.0000.000
188A208ARG10.8810.93631.3227.5377.5370.0000.0000.0000.000
189A209VAL00.0020.00233.481-0.062-0.0620.0000.0000.0000.000
190A210ARG10.8170.89325.70510.57610.5760.0000.0000.0000.000
191A211VAL00.026-0.00527.807-0.193-0.1930.0000.0000.0000.000
192A212ALA0-0.016-0.01329.815-0.107-0.1070.0000.0000.0000.000
193A213SER0-0.041-0.01930.9830.0880.0880.0000.0000.0000.000
194A214TYR0-0.054-0.03225.114-0.129-0.1290.0000.0000.0000.000
195A215MET0-0.024-0.01528.922-0.037-0.0370.0000.0000.0000.000
196A216GLU-1-0.889-0.92430.865-7.993-7.9930.0000.0000.0000.000
197A217ASN0-0.043-0.02628.866-0.226-0.2260.0000.0000.0000.000
198A218ALA00.009-0.00529.146-0.032-0.0320.0000.0000.0000.000
199A219ASN0-0.065-0.05530.1920.0030.0030.0000.0000.0000.000
200A220GLU-1-0.952-0.95633.162-8.487-8.4870.0000.0000.0000.000
201A221GLU-1-1.017-1.00227.641-10.453-10.4530.0000.0000.0000.000
202A222ASP-1-0.966-0.95931.794-8.337-8.3370.0000.0000.0000.000
203A223VAL0-0.085-0.04027.087-0.181-0.1810.0000.0000.0000.000
204A224LEU00.023-0.00729.2940.1060.1060.0000.0000.0000.000
205A225ASN0-0.075-0.03723.3080.2360.2360.0000.0000.0000.000
206A226PHE00.0670.01124.671-0.392-0.3920.0000.0000.0000.000
207A227ALA0-0.0050.01223.5010.2630.2630.0000.0000.0000.000
208A228MET0-0.003-0.00224.545-0.191-0.1910.0000.0000.0000.000
209A229LEU0-0.0010.01221.7000.1690.1690.0000.0000.0000.000
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